fix(doctor): derive orphan stores from registry reconstruction

[ScriptedAlchemy]

Summary

• derive orphan-store warnings from the same read-only registry reconstruction preflight used by migrations
• count only manifests whose project, alias, store, scope, or artifact rows are actually missing
• keep legacy token-accounting cleanup behavior unchanged
• isolate regression fixtures from the repository's shared Git identity marker

Verification

• cargo test orphan_reporting_uses_complete_registry_rows_not_token_accounting --lib
• cargo check --workspace --all-targets --locked
• cargo clippy --workspace --all-targets --locked -- -D warnings
• cargo fmt --check
• live source-built tracedecay doctor: DB integrity ok; false orphan warning absent
• tracedecay tool health --details true: 7107; exact writable branch store; no drift/storage warnings

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Continue diffing after unrelated reconstruction conflicts

In profiles with more than one eligible store manifest, a single conflicting plan (for example an existing registry row for the same root owned by a different project) makes the preflight return an issue here and skips registry_plan_has_missing_rows for every other plan. doctor/health then report zero orphan reconstructable manifests even when other manifests simply have missing registry rows, so one bad manifest hides the actionable repairs this check is meant to surface. Keep the issue but still compute missing rows for non-conflicting plans, or preflight per plan.

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[ScriptedAlchemy]

Valid. Fixed with per-plan preflight plus a conflict+missing regression in #440.